NM_005502.4(ABCA1):c.2320A>C (p.Thr774Pro) AND not provided

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Jan 22, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000590520.15

Allele description [Variation Report for NM_005502.4(ABCA1):c.2320A>C (p.Thr774Pro)]

NM_005502.4(ABCA1):c.2320A>C (p.Thr774Pro)

Gene:

ABCA1:ATP binding cassette subfamily A member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q31.1

Genomic location:

Preferred name:

NM_005502.4(ABCA1):c.2320A>C (p.Thr774Pro)

HGVS:

NC_000009.12:g.104826965T>G
NG_007981.1:g.106191A>C
NM_005502.4:c.2320A>CMANE SELECT
NP_005493.2:p.Thr774Pro
LRG_542t1:c.2320A>C
LRG_542:g.106191A>C
LRG_542p1:p.Thr774Pro
NC_000009.11:g.107589246T>G
NM_005502.3:c.2320A>C
O95477:p.Thr774Pro

Protein change:

T774P

Links:

UniProtKB: O95477#VAR_012622; dbSNP: rs35819696

NCBI 1000 Genomes Browser:

rs35819696

Molecular consequence:

NM_005502.4:c.2320A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000698588	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Dec 5, 2016)	germline	clinical testing	PubMed (10) [See all records that cite these PMIDs] 16226177, 12763760, 15486467, 16806540, 11238261, 16429166, 15520867, 19596329, 18523221, 15297675 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001814305	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Apr 19, 2021)	germline	clinical testing	Citation Link,
SCV001973803	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002390011	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 22, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutation in ABCA1 predicted risk of ischemic heart disease in the Copenhagen City Heart Study Population.

Frikke-Schmidt R, Nordestgaard BG, Schnohr P, Steffensen R, Tybjaerg-Hansen A.

J Am Coll Cardiol. 2005 Oct 18;46(8):1516-20. Epub 2005 Sep 23.

PubMed [citation]

PMID:: 16226177

Efflux and atherosclerosis: the clinical and biochemical impact of variations in the ABCA1 gene.

Singaraja RR, Brunham LR, Visscher H, Kastelein JJ, Hayden MR.

Arterioscler Thromb Vasc Biol. 2003 Aug 1;23(8):1322-32. Epub 2003 May 22. Review.

PubMed [citation]

PMID:: 12763760

See all PubMed Citations (11)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698588.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (10)

Description

Variant summary: The ABCA1 c.2320A>C (p.Thr774Pro) variant involves the alteration of a non-conserved nucleotide. 2/4 in silico tools predict a benign outcome for this variant. This variant was found in 201/121258 control chromosomes (1 homozygote) at a frequency of 0.0016576, which is approximately 133 times the estimated maximal expected allele frequency of a pathogenic ABCA1 variant (0.0000125), suggesting this variant is likely a benign polymorphism. This variant has been shown to not be associated with lipid levels or CAD phenotype (Clee_2001). Further evidence toward benign classification is that one internal sample carries this variant and LDLR c.1291G>A (pathogenic). In addition, the cholesterol efflux was within the normal range in cells from two individuals who had this variant (Cohen_2004). Taken together, this variant is classified as benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001814305.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is associated with the following publications: (PMID: 11238261, 24497850, 15297675)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001973803.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002390011.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine